Multiple sequence alignment - TraesCS1B01G035900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G035900 chr1B 100.000 2366 0 0 1 2366 17134742 17137107 0.000000e+00 4370
1 TraesCS1B01G035900 chr1B 96.314 1655 55 4 360 2012 41212305 41213955 0.000000e+00 2713
2 TraesCS1B01G035900 chr1B 96.254 1655 57 3 360 2012 41174293 41175944 0.000000e+00 2708
3 TraesCS1B01G035900 chr1B 96.774 186 5 1 2181 2366 399808271 399808455 2.280000e-80 309
4 TraesCS1B01G035900 chr1B 96.591 176 6 0 2009 2184 656441533 656441708 2.300000e-75 292
5 TraesCS1B01G035900 chr1B 96.045 177 6 1 2012 2188 41176010 41176185 1.070000e-73 287
6 TraesCS1B01G035900 chr1B 96.045 177 6 1 2012 2188 41214021 41214196 1.070000e-73 287
7 TraesCS1B01G035900 chr1B 95.531 179 8 0 2012 2190 672836825 672836647 1.070000e-73 287
8 TraesCS1B01G035900 chr6B 97.219 2014 52 3 1 2012 617028565 617030576 0.000000e+00 3406
9 TraesCS1B01G035900 chr6B 96.532 173 5 1 2012 2184 617030642 617030813 3.850000e-73 285
10 TraesCS1B01G035900 chr6B 95.954 173 7 0 2012 2184 399206464 399206292 4.980000e-72 281
11 TraesCS1B01G035900 chr2B 97.219 2014 52 3 1 2012 435353322 435351311 0.000000e+00 3406
12 TraesCS1B01G035900 chr2B 95.968 620 22 2 1 618 435372289 435371671 0.000000e+00 1003
13 TraesCS1B01G035900 chr2B 95.789 190 6 2 2178 2366 47510592 47510404 2.950000e-79 305
14 TraesCS1B01G035900 chr2B 97.110 173 5 0 2012 2184 435351245 435351073 2.300000e-75 292
15 TraesCS1B01G035900 chr2B 86.503 163 19 3 166 327 72769587 72769747 2.420000e-40 176
16 TraesCS1B01G035900 chr4A 97.219 2014 47 6 1 2012 602465156 602463150 0.000000e+00 3400
17 TraesCS1B01G035900 chr5A 96.822 2014 57 5 1 2012 692979203 692981211 0.000000e+00 3358
18 TraesCS1B01G035900 chr5A 96.941 1765 50 3 250 2012 693957649 693959411 0.000000e+00 2957
19 TraesCS1B01G035900 chr5B 96.329 2016 68 4 1 2012 576501429 576503442 0.000000e+00 3308
20 TraesCS1B01G035900 chr7B 97.060 1803 48 4 212 2012 709654254 709656053 0.000000e+00 3031
21 TraesCS1B01G035900 chr7B 96.774 186 5 1 2181 2366 650447005 650446821 2.280000e-80 309
22 TraesCS1B01G035900 chr7B 96.277 188 6 1 2179 2366 700946176 700945990 8.210000e-80 307
23 TraesCS1B01G035900 chr7B 97.110 173 5 0 2012 2184 709656119 709656291 2.300000e-75 292
24 TraesCS1B01G035900 chr3B 80.913 723 83 23 164 855 711738738 711738040 9.690000e-144 520
25 TraesCS1B01G035900 chr3B 96.774 186 5 1 2181 2366 787640030 787640214 2.280000e-80 309
26 TraesCS1B01G035900 chr4B 96.774 186 5 1 2181 2366 621827937 621827753 2.280000e-80 309
27 TraesCS1B01G035900 chrUn 96.237 186 6 1 2181 2366 35463613 35463429 1.060000e-78 303
28 TraesCS1B01G035900 chrUn 96.237 186 6 1 2181 2366 230400285 230400101 1.060000e-78 303
29 TraesCS1B01G035900 chrUn 96.237 186 6 1 2181 2366 236959401 236959585 1.060000e-78 303
30 TraesCS1B01G035900 chrUn 96.045 177 6 1 2012 2188 476656490 476656665 1.070000e-73 287


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G035900 chr1B 17134742 17137107 2365 False 4370.0 4370 100.0000 1 2366 1 chr1B.!!$F1 2365
1 TraesCS1B01G035900 chr1B 41212305 41214196 1891 False 1500.0 2713 96.1795 360 2188 2 chr1B.!!$F5 1828
2 TraesCS1B01G035900 chr1B 41174293 41176185 1892 False 1497.5 2708 96.1495 360 2188 2 chr1B.!!$F4 1828
3 TraesCS1B01G035900 chr6B 617028565 617030813 2248 False 1845.5 3406 96.8755 1 2184 2 chr6B.!!$F1 2183
4 TraesCS1B01G035900 chr2B 435351073 435353322 2249 True 1849.0 3406 97.1645 1 2184 2 chr2B.!!$R3 2183
5 TraesCS1B01G035900 chr2B 435371671 435372289 618 True 1003.0 1003 95.9680 1 618 1 chr2B.!!$R2 617
6 TraesCS1B01G035900 chr4A 602463150 602465156 2006 True 3400.0 3400 97.2190 1 2012 1 chr4A.!!$R1 2011
7 TraesCS1B01G035900 chr5A 692979203 692981211 2008 False 3358.0 3358 96.8220 1 2012 1 chr5A.!!$F1 2011
8 TraesCS1B01G035900 chr5A 693957649 693959411 1762 False 2957.0 2957 96.9410 250 2012 1 chr5A.!!$F2 1762
9 TraesCS1B01G035900 chr5B 576501429 576503442 2013 False 3308.0 3308 96.3290 1 2012 1 chr5B.!!$F1 2011
10 TraesCS1B01G035900 chr7B 709654254 709656291 2037 False 1661.5 3031 97.0850 212 2184 2 chr7B.!!$F1 1972
11 TraesCS1B01G035900 chr3B 711738040 711738738 698 True 520.0 520 80.9130 164 855 1 chr3B.!!$R1 691

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
840 875 1.401761 TCTGCTTGCCTGCTTCAAAA 58.598 45.0 0.0 0.0 0.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2248 2353 0.033504 TGAAGGTCACGACTGGCTTC 59.966 55.0 0.0 7.38 31.86 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 100 4.401022 TCGTAAGGGTGAAGAGTTGACTA 58.599 43.478 0.00 0.00 38.47 2.59
148 151 3.646162 TGGCAAGAAGACTGGTTTCTCTA 59.354 43.478 0.00 0.00 33.92 2.43
172 175 4.884247 GCCAGTTAAGAAGGCGATAGTAT 58.116 43.478 0.00 0.00 38.86 2.12
258 261 9.836864 ATTACATTATATGACTTCTGCTTGACA 57.163 29.630 0.00 0.00 0.00 3.58
276 279 6.202570 GCTTGACAGATTTGATAGAGATGGTC 59.797 42.308 0.00 0.00 0.00 4.02
378 409 5.798125 TTCATTTTGGTACTGGAAATGCA 57.202 34.783 16.93 0.00 39.44 3.96
381 412 4.329462 TTTTGGTACTGGAAATGCAACC 57.671 40.909 0.00 0.00 0.00 3.77
402 433 7.201548 GCAACCATATTCAGGCAATTTTAGTTG 60.202 37.037 0.00 0.00 33.35 3.16
521 553 3.434984 GCATCTATCTTCCCATCTTTCGC 59.565 47.826 0.00 0.00 0.00 4.70
554 589 7.953158 AACTGTCATTTCATATACGATCTGG 57.047 36.000 0.00 0.00 0.00 3.86
637 672 2.401583 ACATATGCGCTCCTGAAACA 57.598 45.000 9.73 0.00 0.00 2.83
840 875 1.401761 TCTGCTTGCCTGCTTCAAAA 58.598 45.000 0.00 0.00 0.00 2.44
1122 1159 1.188219 TTGGCCTTGAGTCGAGCTCT 61.188 55.000 12.85 0.00 44.41 4.09
1163 1200 1.428219 CAGCTGCTTTGGATGCTCG 59.572 57.895 0.00 0.00 33.03 5.03
1184 1221 6.403418 GCTCGTGTACAAGAACTAGAGTACAT 60.403 42.308 12.62 0.00 45.70 2.29
1226 1263 0.809241 GCTGAGTTGATGCGAGAGGG 60.809 60.000 0.00 0.00 0.00 4.30
1359 1396 6.884295 TCATGGATCTGTTCGAAGGTAAAATT 59.116 34.615 0.00 0.00 0.00 1.82
1755 1793 5.330233 TCGTCTCAAGGCCCAATATAGATA 58.670 41.667 0.00 0.00 0.00 1.98
2029 2134 1.147473 CAAATTTTGGTCAAGGGCGC 58.853 50.000 0.00 0.00 0.00 6.53
2061 2166 4.830826 AATTCCAGAAAAGGTCACGTTC 57.169 40.909 0.00 0.00 0.00 3.95
2066 2171 2.605818 CAGAAAAGGTCACGTTCGTTCA 59.394 45.455 0.00 0.00 0.00 3.18
2078 2183 2.409752 CGTTCGTTCATTCTTGACGGTG 60.410 50.000 0.00 0.00 31.58 4.94
2184 2289 5.796350 ATTGACCGTATTTCTTGTAGTGC 57.204 39.130 0.00 0.00 0.00 4.40
2188 2293 4.827692 ACCGTATTTCTTGTAGTGCATGA 58.172 39.130 0.00 0.00 0.00 3.07
2189 2294 4.870426 ACCGTATTTCTTGTAGTGCATGAG 59.130 41.667 0.00 0.00 33.60 2.90
2190 2295 5.109210 CCGTATTTCTTGTAGTGCATGAGA 58.891 41.667 0.00 0.00 33.60 3.27
2191 2296 5.005779 CCGTATTTCTTGTAGTGCATGAGAC 59.994 44.000 0.00 0.00 33.60 3.36
2192 2297 5.807520 CGTATTTCTTGTAGTGCATGAGACT 59.192 40.000 0.00 0.00 33.60 3.24
2193 2298 6.311445 CGTATTTCTTGTAGTGCATGAGACTT 59.689 38.462 0.00 0.00 33.60 3.01
2194 2299 7.148573 CGTATTTCTTGTAGTGCATGAGACTTT 60.149 37.037 0.00 0.00 33.60 2.66
2195 2300 9.151471 GTATTTCTTGTAGTGCATGAGACTTTA 57.849 33.333 0.00 0.00 33.60 1.85
2196 2301 7.658179 TTTCTTGTAGTGCATGAGACTTTAG 57.342 36.000 0.00 0.00 33.60 1.85
2197 2302 5.724328 TCTTGTAGTGCATGAGACTTTAGG 58.276 41.667 0.00 0.00 0.00 2.69
2198 2303 5.246203 TCTTGTAGTGCATGAGACTTTAGGT 59.754 40.000 0.00 0.00 0.00 3.08
2199 2304 5.483685 TGTAGTGCATGAGACTTTAGGTT 57.516 39.130 0.00 0.00 0.00 3.50
2200 2305 5.479306 TGTAGTGCATGAGACTTTAGGTTC 58.521 41.667 0.00 0.00 0.00 3.62
2201 2306 4.899352 AGTGCATGAGACTTTAGGTTCT 57.101 40.909 0.00 0.00 0.00 3.01
2202 2307 4.573900 AGTGCATGAGACTTTAGGTTCTG 58.426 43.478 0.00 0.00 0.00 3.02
2203 2308 4.284490 AGTGCATGAGACTTTAGGTTCTGA 59.716 41.667 0.00 0.00 0.00 3.27
2204 2309 4.997395 GTGCATGAGACTTTAGGTTCTGAA 59.003 41.667 0.00 0.00 0.00 3.02
2205 2310 5.470098 GTGCATGAGACTTTAGGTTCTGAAA 59.530 40.000 0.00 0.00 0.00 2.69
2206 2311 5.470098 TGCATGAGACTTTAGGTTCTGAAAC 59.530 40.000 0.00 0.00 34.46 2.78
2207 2312 5.703130 GCATGAGACTTTAGGTTCTGAAACT 59.297 40.000 13.23 13.23 35.61 2.66
2208 2313 6.205658 GCATGAGACTTTAGGTTCTGAAACTT 59.794 38.462 13.96 0.00 35.61 2.66
2209 2314 7.255277 GCATGAGACTTTAGGTTCTGAAACTTT 60.255 37.037 13.96 0.00 35.61 2.66
2210 2315 8.624776 CATGAGACTTTAGGTTCTGAAACTTTT 58.375 33.333 13.96 0.00 35.61 2.27
2211 2316 8.575649 TGAGACTTTAGGTTCTGAAACTTTTT 57.424 30.769 13.96 0.00 35.61 1.94
2212 2317 8.674607 TGAGACTTTAGGTTCTGAAACTTTTTC 58.325 33.333 13.96 5.73 35.61 2.29
2213 2318 8.809468 AGACTTTAGGTTCTGAAACTTTTTCT 57.191 30.769 13.96 7.80 35.61 2.52
2214 2319 8.894731 AGACTTTAGGTTCTGAAACTTTTTCTC 58.105 33.333 13.96 3.03 35.61 2.87
2215 2320 8.809468 ACTTTAGGTTCTGAAACTTTTTCTCT 57.191 30.769 13.96 0.00 35.61 3.10
2216 2321 9.901172 ACTTTAGGTTCTGAAACTTTTTCTCTA 57.099 29.630 13.96 0.00 35.61 2.43
2218 2323 8.672823 TTAGGTTCTGAAACTTTTTCTCTACC 57.327 34.615 13.96 0.00 35.61 3.18
2219 2324 6.659824 AGGTTCTGAAACTTTTTCTCTACCA 58.340 36.000 1.18 0.00 35.61 3.25
2220 2325 7.290813 AGGTTCTGAAACTTTTTCTCTACCAT 58.709 34.615 1.18 0.00 35.61 3.55
2221 2326 8.437575 AGGTTCTGAAACTTTTTCTCTACCATA 58.562 33.333 1.18 0.00 35.61 2.74
2222 2327 9.232473 GGTTCTGAAACTTTTTCTCTACCATAT 57.768 33.333 0.00 0.00 35.61 1.78
2251 2356 9.640963 ATTATTCCCTTTATATTCGACGAGAAG 57.359 33.333 0.00 0.00 42.92 2.85
2252 2357 4.868067 TCCCTTTATATTCGACGAGAAGC 58.132 43.478 0.00 0.00 42.92 3.86
2253 2358 3.988517 CCCTTTATATTCGACGAGAAGCC 59.011 47.826 0.00 0.00 42.92 4.35
2254 2359 4.500887 CCCTTTATATTCGACGAGAAGCCA 60.501 45.833 0.00 0.00 42.92 4.75
2255 2360 4.681942 CCTTTATATTCGACGAGAAGCCAG 59.318 45.833 0.00 0.00 42.92 4.85
2256 2361 4.913335 TTATATTCGACGAGAAGCCAGT 57.087 40.909 0.00 0.00 42.92 4.00
2257 2362 2.846039 TATTCGACGAGAAGCCAGTC 57.154 50.000 0.00 0.00 42.92 3.51
2262 2367 4.154613 CGAGAAGCCAGTCGTGAC 57.845 61.111 0.00 0.00 0.00 3.67
2263 2368 1.444553 CGAGAAGCCAGTCGTGACC 60.445 63.158 0.00 0.00 0.00 4.02
2264 2369 1.867919 CGAGAAGCCAGTCGTGACCT 61.868 60.000 0.00 0.00 0.00 3.85
2265 2370 0.318762 GAGAAGCCAGTCGTGACCTT 59.681 55.000 0.00 0.00 0.00 3.50
2266 2371 0.318762 AGAAGCCAGTCGTGACCTTC 59.681 55.000 8.54 8.54 34.55 3.46
2267 2372 0.033504 GAAGCCAGTCGTGACCTTCA 59.966 55.000 10.63 0.00 34.52 3.02
2268 2373 0.687354 AAGCCAGTCGTGACCTTCAT 59.313 50.000 0.00 0.00 0.00 2.57
2269 2374 1.557099 AGCCAGTCGTGACCTTCATA 58.443 50.000 0.00 0.00 0.00 2.15
2270 2375 1.204941 AGCCAGTCGTGACCTTCATAC 59.795 52.381 0.00 0.00 0.00 2.39
2271 2376 1.204941 GCCAGTCGTGACCTTCATACT 59.795 52.381 0.00 0.00 0.00 2.12
2272 2377 2.426024 GCCAGTCGTGACCTTCATACTA 59.574 50.000 0.00 0.00 0.00 1.82
2273 2378 3.119245 GCCAGTCGTGACCTTCATACTAA 60.119 47.826 0.00 0.00 0.00 2.24
2274 2379 4.673441 CCAGTCGTGACCTTCATACTAAG 58.327 47.826 0.00 0.00 0.00 2.18
2275 2380 4.106197 CAGTCGTGACCTTCATACTAAGC 58.894 47.826 0.00 0.00 0.00 3.09
2276 2381 3.762288 AGTCGTGACCTTCATACTAAGCA 59.238 43.478 0.00 0.00 0.00 3.91
2277 2382 4.106197 GTCGTGACCTTCATACTAAGCAG 58.894 47.826 0.00 0.00 0.00 4.24
2278 2383 3.130516 TCGTGACCTTCATACTAAGCAGG 59.869 47.826 0.00 0.00 0.00 4.85
2279 2384 3.198872 GTGACCTTCATACTAAGCAGGC 58.801 50.000 0.00 0.00 0.00 4.85
2280 2385 2.837591 TGACCTTCATACTAAGCAGGCA 59.162 45.455 0.00 0.00 0.00 4.75
2281 2386 3.455910 TGACCTTCATACTAAGCAGGCAT 59.544 43.478 0.00 0.00 0.00 4.40
2282 2387 4.080356 TGACCTTCATACTAAGCAGGCATT 60.080 41.667 0.00 0.00 0.00 3.56
2283 2388 4.455606 ACCTTCATACTAAGCAGGCATTC 58.544 43.478 0.00 0.00 0.00 2.67
2284 2389 4.080356 ACCTTCATACTAAGCAGGCATTCA 60.080 41.667 0.00 0.00 0.00 2.57
2285 2390 4.883585 CCTTCATACTAAGCAGGCATTCAA 59.116 41.667 0.00 0.00 0.00 2.69
2286 2391 5.357878 CCTTCATACTAAGCAGGCATTCAAA 59.642 40.000 0.00 0.00 0.00 2.69
2287 2392 6.441093 TTCATACTAAGCAGGCATTCAAAG 57.559 37.500 0.00 0.00 0.00 2.77
2288 2393 5.744171 TCATACTAAGCAGGCATTCAAAGA 58.256 37.500 0.00 0.00 0.00 2.52
2289 2394 6.179756 TCATACTAAGCAGGCATTCAAAGAA 58.820 36.000 0.00 0.00 0.00 2.52
2290 2395 6.317140 TCATACTAAGCAGGCATTCAAAGAAG 59.683 38.462 0.00 0.00 0.00 2.85
2291 2396 4.655963 ACTAAGCAGGCATTCAAAGAAGA 58.344 39.130 0.00 0.00 0.00 2.87
2292 2397 5.259632 ACTAAGCAGGCATTCAAAGAAGAT 58.740 37.500 0.00 0.00 0.00 2.40
2293 2398 5.713861 ACTAAGCAGGCATTCAAAGAAGATT 59.286 36.000 0.00 0.00 0.00 2.40
2294 2399 5.479124 AAGCAGGCATTCAAAGAAGATTT 57.521 34.783 0.00 0.00 0.00 2.17
2295 2400 6.594788 AAGCAGGCATTCAAAGAAGATTTA 57.405 33.333 0.00 0.00 0.00 1.40
2296 2401 5.958955 AGCAGGCATTCAAAGAAGATTTAC 58.041 37.500 0.00 0.00 0.00 2.01
2297 2402 5.713861 AGCAGGCATTCAAAGAAGATTTACT 59.286 36.000 0.00 0.00 0.00 2.24
2298 2403 6.210185 AGCAGGCATTCAAAGAAGATTTACTT 59.790 34.615 0.00 0.00 42.03 2.24
2316 2421 7.964604 TTTACTTCTCTTCTTTGGTAAGAGC 57.035 36.000 7.77 0.00 46.29 4.09
2317 2422 4.561105 ACTTCTCTTCTTTGGTAAGAGCG 58.439 43.478 7.77 4.82 46.29 5.03
2318 2423 4.039366 ACTTCTCTTCTTTGGTAAGAGCGT 59.961 41.667 7.77 5.32 46.29 5.07
2319 2424 5.243283 ACTTCTCTTCTTTGGTAAGAGCGTA 59.757 40.000 7.77 0.00 46.29 4.42
2320 2425 5.312120 TCTCTTCTTTGGTAAGAGCGTAG 57.688 43.478 7.77 0.00 46.29 3.51
2333 2438 3.915575 CGTAGCTGGTAGGACCGT 58.084 61.111 0.00 0.00 42.58 4.83
2334 2439 1.726265 CGTAGCTGGTAGGACCGTC 59.274 63.158 0.00 0.00 42.58 4.79
2335 2440 1.028330 CGTAGCTGGTAGGACCGTCA 61.028 60.000 0.00 0.00 42.58 4.35
2336 2441 1.400737 GTAGCTGGTAGGACCGTCAT 58.599 55.000 0.00 0.00 42.58 3.06
2337 2442 2.579873 GTAGCTGGTAGGACCGTCATA 58.420 52.381 0.00 0.00 42.58 2.15
2338 2443 1.400737 AGCTGGTAGGACCGTCATAC 58.599 55.000 13.74 13.74 42.58 2.39
2339 2444 1.063867 AGCTGGTAGGACCGTCATACT 60.064 52.381 19.69 2.73 42.58 2.12
2340 2445 1.067212 GCTGGTAGGACCGTCATACTG 59.933 57.143 19.69 14.53 42.58 2.74
2341 2446 1.067212 CTGGTAGGACCGTCATACTGC 59.933 57.143 19.69 7.69 42.58 4.40
2342 2447 1.341679 TGGTAGGACCGTCATACTGCT 60.342 52.381 19.69 1.42 42.58 4.24
2343 2448 1.755380 GGTAGGACCGTCATACTGCTT 59.245 52.381 19.69 0.00 34.41 3.91
2344 2449 2.167900 GGTAGGACCGTCATACTGCTTT 59.832 50.000 19.69 0.00 34.41 3.51
2345 2450 2.386661 AGGACCGTCATACTGCTTTG 57.613 50.000 0.00 0.00 0.00 2.77
2346 2451 1.066143 AGGACCGTCATACTGCTTTGG 60.066 52.381 0.00 0.00 0.00 3.28
2347 2452 1.066430 GGACCGTCATACTGCTTTGGA 60.066 52.381 0.00 0.00 0.00 3.53
2348 2453 2.271800 GACCGTCATACTGCTTTGGAG 58.728 52.381 0.00 0.00 0.00 3.86
2349 2454 1.066143 ACCGTCATACTGCTTTGGAGG 60.066 52.381 0.00 0.00 0.00 4.30
2350 2455 1.009829 CGTCATACTGCTTTGGAGGC 58.990 55.000 0.00 0.00 0.00 4.70
2351 2456 1.675714 CGTCATACTGCTTTGGAGGCA 60.676 52.381 0.00 0.00 38.10 4.75
2352 2457 2.648059 GTCATACTGCTTTGGAGGCAT 58.352 47.619 0.00 0.00 39.07 4.40
2353 2458 2.357009 GTCATACTGCTTTGGAGGCATG 59.643 50.000 0.00 0.00 39.07 4.06
2354 2459 1.066605 CATACTGCTTTGGAGGCATGC 59.933 52.381 9.90 9.90 39.07 4.06
2355 2460 0.680921 TACTGCTTTGGAGGCATGCC 60.681 55.000 30.12 30.12 39.07 4.40
2356 2461 3.060020 CTGCTTTGGAGGCATGCCG 62.060 63.158 30.50 16.42 41.95 5.69
2357 2462 3.064324 GCTTTGGAGGCATGCCGT 61.064 61.111 30.50 18.98 41.95 5.68
2358 2463 3.056313 GCTTTGGAGGCATGCCGTC 62.056 63.158 30.50 25.15 41.95 4.79
2359 2464 1.377725 CTTTGGAGGCATGCCGTCT 60.378 57.895 30.50 14.41 41.95 4.18
2360 2465 0.962356 CTTTGGAGGCATGCCGTCTT 60.962 55.000 30.50 14.00 41.95 3.01
2361 2466 0.539438 TTTGGAGGCATGCCGTCTTT 60.539 50.000 30.50 13.57 41.95 2.52
2362 2467 0.539438 TTGGAGGCATGCCGTCTTTT 60.539 50.000 30.50 12.74 41.95 2.27
2363 2468 0.539438 TGGAGGCATGCCGTCTTTTT 60.539 50.000 30.50 11.91 41.95 1.94
2364 2469 0.171231 GGAGGCATGCCGTCTTTTTC 59.829 55.000 30.50 19.83 41.95 2.29
2365 2470 0.179189 GAGGCATGCCGTCTTTTTCG 60.179 55.000 30.50 0.00 41.95 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 151 2.789409 ATCGCCTTCTTAACTGGCTT 57.211 45.000 0.00 0.00 44.09 4.35
172 175 9.100554 TCAACACGAAAAAGAATACTAGAAACA 57.899 29.630 0.00 0.00 0.00 2.83
258 261 9.745018 TTTGAAAAGACCATCTCTATCAAATCT 57.255 29.630 0.00 0.00 38.64 2.40
378 409 7.906327 ACAACTAAAATTGCCTGAATATGGTT 58.094 30.769 0.00 0.00 32.47 3.67
381 412 8.761575 ACAACAACTAAAATTGCCTGAATATG 57.238 30.769 0.00 0.00 32.47 1.78
402 433 1.103398 ACCTGCTGGACTGCAACAAC 61.103 55.000 17.64 0.00 42.83 3.32
554 589 6.817765 TCCACAAGTCCTAAACATTTCATC 57.182 37.500 0.00 0.00 0.00 2.92
637 672 6.326064 ACATGGAGCAGAGAAGAATGTAGTAT 59.674 38.462 0.00 0.00 0.00 2.12
1122 1159 6.524734 TGCAGATCTGTTGAACTTCTTCTTA 58.475 36.000 23.38 0.00 0.00 2.10
1163 1200 6.622549 AGCATGTACTCTAGTTCTTGTACAC 58.377 40.000 0.00 0.00 44.94 2.90
1184 1221 0.900182 TCGCCTCTCCTTCTCAAGCA 60.900 55.000 0.00 0.00 0.00 3.91
1226 1263 2.851195 TCTTCTTGACCTCAACAAGCC 58.149 47.619 0.00 0.00 42.76 4.35
1359 1396 3.404224 TCAACCACGCCATACTAAACA 57.596 42.857 0.00 0.00 0.00 2.83
1476 1513 4.985538 ACACAACCTCATCAAACCATAGT 58.014 39.130 0.00 0.00 0.00 2.12
1563 1600 4.460382 AGTTCATAAGATGCACCAACCAAG 59.540 41.667 0.00 0.00 0.00 3.61
1672 1709 4.217550 GCCAATAACCAACAGTAGCTCAAA 59.782 41.667 0.00 0.00 0.00 2.69
1933 1972 4.954092 GGATCAGTCCAAATCAGTTGTC 57.046 45.455 0.00 0.00 44.42 3.18
2029 2134 8.115490 ACCTTTTCTGGAATTTTAGTCATGAG 57.885 34.615 0.00 0.00 0.00 2.90
2061 2166 3.169207 GTTCACCGTCAAGAATGAACG 57.831 47.619 0.65 0.00 40.95 3.95
2066 2171 3.560068 GTCAACAGTTCACCGTCAAGAAT 59.440 43.478 0.00 0.00 0.00 2.40
2078 2183 4.537015 CAAATTCGGAAGGTCAACAGTTC 58.463 43.478 0.00 0.00 0.00 3.01
2184 2289 7.736447 AAGTTTCAGAACCTAAAGTCTCATG 57.264 36.000 0.00 0.00 36.39 3.07
2188 2293 8.809468 AGAAAAAGTTTCAGAACCTAAAGTCT 57.191 30.769 3.74 0.00 36.39 3.24
2189 2294 8.894731 AGAGAAAAAGTTTCAGAACCTAAAGTC 58.105 33.333 3.74 0.00 36.39 3.01
2190 2295 8.809468 AGAGAAAAAGTTTCAGAACCTAAAGT 57.191 30.769 3.74 0.00 36.39 2.66
2192 2297 9.117183 GGTAGAGAAAAAGTTTCAGAACCTAAA 57.883 33.333 3.74 0.00 36.39 1.85
2193 2298 8.269317 TGGTAGAGAAAAAGTTTCAGAACCTAA 58.731 33.333 14.26 0.70 36.39 2.69
2194 2299 7.798071 TGGTAGAGAAAAAGTTTCAGAACCTA 58.202 34.615 14.26 0.00 36.39 3.08
2195 2300 6.659824 TGGTAGAGAAAAAGTTTCAGAACCT 58.340 36.000 14.26 0.00 36.39 3.50
2196 2301 6.937436 TGGTAGAGAAAAAGTTTCAGAACC 57.063 37.500 3.74 7.25 36.39 3.62
2225 2330 9.640963 CTTCTCGTCGAATATAAAGGGAATAAT 57.359 33.333 0.00 0.00 0.00 1.28
2226 2331 7.597743 GCTTCTCGTCGAATATAAAGGGAATAA 59.402 37.037 0.00 0.00 0.00 1.40
2227 2332 7.088905 GCTTCTCGTCGAATATAAAGGGAATA 58.911 38.462 0.00 0.00 0.00 1.75
2228 2333 5.927115 GCTTCTCGTCGAATATAAAGGGAAT 59.073 40.000 0.00 0.00 0.00 3.01
2229 2334 5.287226 GCTTCTCGTCGAATATAAAGGGAA 58.713 41.667 0.00 0.00 0.00 3.97
2230 2335 4.261909 GGCTTCTCGTCGAATATAAAGGGA 60.262 45.833 0.00 0.00 0.00 4.20
2231 2336 3.988517 GGCTTCTCGTCGAATATAAAGGG 59.011 47.826 0.00 0.00 0.00 3.95
2232 2337 4.617959 TGGCTTCTCGTCGAATATAAAGG 58.382 43.478 0.00 0.00 0.00 3.11
2233 2338 5.282510 ACTGGCTTCTCGTCGAATATAAAG 58.717 41.667 0.00 0.00 0.00 1.85
2234 2339 5.258456 ACTGGCTTCTCGTCGAATATAAA 57.742 39.130 0.00 0.00 0.00 1.40
2235 2340 4.856664 GACTGGCTTCTCGTCGAATATAA 58.143 43.478 0.00 0.00 0.00 0.98
2236 2341 4.485024 GACTGGCTTCTCGTCGAATATA 57.515 45.455 0.00 0.00 0.00 0.86
2237 2342 3.357166 GACTGGCTTCTCGTCGAATAT 57.643 47.619 0.00 0.00 0.00 1.28
2238 2343 2.846039 GACTGGCTTCTCGTCGAATA 57.154 50.000 0.00 0.00 0.00 1.75
2239 2344 3.723554 GACTGGCTTCTCGTCGAAT 57.276 52.632 0.00 0.00 0.00 3.34
2243 2348 0.729816 GTCACGACTGGCTTCTCGTC 60.730 60.000 0.00 0.00 41.13 4.20
2244 2349 1.286260 GTCACGACTGGCTTCTCGT 59.714 57.895 0.00 0.00 43.83 4.18
2245 2350 1.444553 GGTCACGACTGGCTTCTCG 60.445 63.158 0.00 0.00 35.96 4.04
2246 2351 0.318762 AAGGTCACGACTGGCTTCTC 59.681 55.000 0.00 0.00 0.00 2.87
2247 2352 0.318762 GAAGGTCACGACTGGCTTCT 59.681 55.000 0.00 0.00 29.99 2.85
2248 2353 0.033504 TGAAGGTCACGACTGGCTTC 59.966 55.000 0.00 7.38 31.86 3.86
2249 2354 0.687354 ATGAAGGTCACGACTGGCTT 59.313 50.000 0.00 0.00 0.00 4.35
2250 2355 1.204941 GTATGAAGGTCACGACTGGCT 59.795 52.381 0.00 0.00 0.00 4.75
2251 2356 1.204941 AGTATGAAGGTCACGACTGGC 59.795 52.381 0.00 0.00 28.22 4.85
2252 2357 4.673441 CTTAGTATGAAGGTCACGACTGG 58.327 47.826 0.00 0.00 31.00 4.00
2253 2358 4.106197 GCTTAGTATGAAGGTCACGACTG 58.894 47.826 0.00 0.00 31.00 3.51
2254 2359 3.762288 TGCTTAGTATGAAGGTCACGACT 59.238 43.478 0.00 1.56 32.57 4.18
2255 2360 4.106029 TGCTTAGTATGAAGGTCACGAC 57.894 45.455 0.00 0.00 0.00 4.34
2256 2361 3.130516 CCTGCTTAGTATGAAGGTCACGA 59.869 47.826 2.33 0.00 0.00 4.35
2257 2362 3.448686 CCTGCTTAGTATGAAGGTCACG 58.551 50.000 2.33 0.00 0.00 4.35
2258 2363 3.198872 GCCTGCTTAGTATGAAGGTCAC 58.801 50.000 10.99 0.00 0.00 3.67
2259 2364 2.837591 TGCCTGCTTAGTATGAAGGTCA 59.162 45.455 10.99 7.29 0.00 4.02
2260 2365 3.543680 TGCCTGCTTAGTATGAAGGTC 57.456 47.619 10.99 5.20 0.00 3.85
2261 2366 4.080356 TGAATGCCTGCTTAGTATGAAGGT 60.080 41.667 10.99 0.00 0.00 3.50
2262 2367 4.454678 TGAATGCCTGCTTAGTATGAAGG 58.545 43.478 5.79 5.79 0.00 3.46
2263 2368 6.317140 TCTTTGAATGCCTGCTTAGTATGAAG 59.683 38.462 0.00 0.00 0.00 3.02
2264 2369 6.179756 TCTTTGAATGCCTGCTTAGTATGAA 58.820 36.000 0.00 0.00 0.00 2.57
2265 2370 5.744171 TCTTTGAATGCCTGCTTAGTATGA 58.256 37.500 0.00 0.00 0.00 2.15
2266 2371 6.317140 TCTTCTTTGAATGCCTGCTTAGTATG 59.683 38.462 0.00 0.00 0.00 2.39
2267 2372 6.418101 TCTTCTTTGAATGCCTGCTTAGTAT 58.582 36.000 0.00 0.00 0.00 2.12
2268 2373 5.804639 TCTTCTTTGAATGCCTGCTTAGTA 58.195 37.500 0.00 0.00 0.00 1.82
2269 2374 4.655963 TCTTCTTTGAATGCCTGCTTAGT 58.344 39.130 0.00 0.00 0.00 2.24
2270 2375 5.831702 ATCTTCTTTGAATGCCTGCTTAG 57.168 39.130 0.00 0.00 0.00 2.18
2271 2376 6.594788 AAATCTTCTTTGAATGCCTGCTTA 57.405 33.333 0.00 0.00 0.00 3.09
2272 2377 5.479124 AAATCTTCTTTGAATGCCTGCTT 57.521 34.783 0.00 0.00 0.00 3.91
2273 2378 5.713861 AGTAAATCTTCTTTGAATGCCTGCT 59.286 36.000 0.00 0.00 0.00 4.24
2274 2379 5.958955 AGTAAATCTTCTTTGAATGCCTGC 58.041 37.500 0.00 0.00 0.00 4.85
2300 2405 3.510360 AGCTACGCTCTTACCAAAGAAGA 59.490 43.478 0.00 0.00 41.19 2.87
2301 2406 3.614616 CAGCTACGCTCTTACCAAAGAAG 59.385 47.826 0.00 0.00 41.19 2.85
2302 2407 3.585862 CAGCTACGCTCTTACCAAAGAA 58.414 45.455 0.00 0.00 41.19 2.52
2303 2408 2.094182 CCAGCTACGCTCTTACCAAAGA 60.094 50.000 0.00 0.00 36.40 2.52
2304 2409 2.271800 CCAGCTACGCTCTTACCAAAG 58.728 52.381 0.00 0.00 36.40 2.77
2305 2410 1.621814 ACCAGCTACGCTCTTACCAAA 59.378 47.619 0.00 0.00 36.40 3.28
2306 2411 1.263356 ACCAGCTACGCTCTTACCAA 58.737 50.000 0.00 0.00 36.40 3.67
2307 2412 2.022195 CTACCAGCTACGCTCTTACCA 58.978 52.381 0.00 0.00 36.40 3.25
2308 2413 1.337387 CCTACCAGCTACGCTCTTACC 59.663 57.143 0.00 0.00 36.40 2.85
2309 2414 2.033174 GTCCTACCAGCTACGCTCTTAC 59.967 54.545 0.00 0.00 36.40 2.34
2310 2415 2.295885 GTCCTACCAGCTACGCTCTTA 58.704 52.381 0.00 0.00 36.40 2.10
2311 2416 1.104630 GTCCTACCAGCTACGCTCTT 58.895 55.000 0.00 0.00 36.40 2.85
2312 2417 0.752376 GGTCCTACCAGCTACGCTCT 60.752 60.000 0.00 0.00 36.40 4.09
2313 2418 1.734748 GGTCCTACCAGCTACGCTC 59.265 63.158 0.00 0.00 36.40 5.03
2314 2419 2.119655 CGGTCCTACCAGCTACGCT 61.120 63.158 0.00 0.00 38.47 5.07
2315 2420 2.333706 GACGGTCCTACCAGCTACGC 62.334 65.000 0.00 0.00 38.47 4.42
2316 2421 1.028330 TGACGGTCCTACCAGCTACG 61.028 60.000 5.55 0.00 38.47 3.51
2317 2422 1.400737 ATGACGGTCCTACCAGCTAC 58.599 55.000 5.55 0.00 38.47 3.58
2318 2423 2.174210 AGTATGACGGTCCTACCAGCTA 59.826 50.000 16.69 0.00 38.47 3.32
2319 2424 1.063867 AGTATGACGGTCCTACCAGCT 60.064 52.381 16.69 0.14 38.47 4.24
2320 2425 1.067212 CAGTATGACGGTCCTACCAGC 59.933 57.143 16.69 0.00 39.69 4.85
2321 2426 1.067212 GCAGTATGACGGTCCTACCAG 59.933 57.143 16.69 12.20 39.69 4.00
2322 2427 1.108776 GCAGTATGACGGTCCTACCA 58.891 55.000 16.69 0.00 39.69 3.25
2323 2428 1.400737 AGCAGTATGACGGTCCTACC 58.599 55.000 16.69 6.04 39.69 3.18
2324 2429 3.187700 CAAAGCAGTATGACGGTCCTAC 58.812 50.000 13.63 13.63 39.69 3.18
2325 2430 2.167693 CCAAAGCAGTATGACGGTCCTA 59.832 50.000 5.55 0.00 39.69 2.94
2326 2431 1.066143 CCAAAGCAGTATGACGGTCCT 60.066 52.381 5.55 0.00 39.69 3.85
2327 2432 1.066430 TCCAAAGCAGTATGACGGTCC 60.066 52.381 5.55 0.00 39.69 4.46
2328 2433 2.271800 CTCCAAAGCAGTATGACGGTC 58.728 52.381 0.00 0.00 39.69 4.79
2329 2434 1.066143 CCTCCAAAGCAGTATGACGGT 60.066 52.381 0.00 0.00 39.69 4.83
2330 2435 1.656652 CCTCCAAAGCAGTATGACGG 58.343 55.000 0.00 0.00 39.69 4.79
2331 2436 1.009829 GCCTCCAAAGCAGTATGACG 58.990 55.000 0.00 0.00 39.69 4.35
2332 2437 2.113860 TGCCTCCAAAGCAGTATGAC 57.886 50.000 0.00 0.00 39.69 3.06
2333 2438 2.646930 CATGCCTCCAAAGCAGTATGA 58.353 47.619 0.00 0.00 44.90 2.15
2334 2439 1.066605 GCATGCCTCCAAAGCAGTATG 59.933 52.381 6.36 0.00 44.90 2.39
2335 2440 1.396653 GCATGCCTCCAAAGCAGTAT 58.603 50.000 6.36 0.00 44.90 2.12
2336 2441 0.680921 GGCATGCCTCCAAAGCAGTA 60.681 55.000 29.98 0.00 44.90 2.74
2337 2442 1.980772 GGCATGCCTCCAAAGCAGT 60.981 57.895 29.98 0.00 44.90 4.40
2338 2443 2.890371 GGCATGCCTCCAAAGCAG 59.110 61.111 29.98 0.00 44.90 4.24
2339 2444 3.063704 CGGCATGCCTCCAAAGCA 61.064 61.111 33.07 0.00 45.94 3.91
2340 2445 3.056313 GACGGCATGCCTCCAAAGC 62.056 63.158 33.07 11.18 0.00 3.51
2341 2446 0.962356 AAGACGGCATGCCTCCAAAG 60.962 55.000 33.07 19.22 0.00 2.77
2342 2447 0.539438 AAAGACGGCATGCCTCCAAA 60.539 50.000 33.07 0.00 0.00 3.28
2343 2448 0.539438 AAAAGACGGCATGCCTCCAA 60.539 50.000 33.07 0.00 0.00 3.53
2344 2449 0.539438 AAAAAGACGGCATGCCTCCA 60.539 50.000 33.07 0.00 0.00 3.86
2345 2450 0.171231 GAAAAAGACGGCATGCCTCC 59.829 55.000 33.07 23.40 0.00 4.30
2346 2451 0.179189 CGAAAAAGACGGCATGCCTC 60.179 55.000 33.07 26.60 0.00 4.70
2347 2452 1.875963 CGAAAAAGACGGCATGCCT 59.124 52.632 33.07 20.54 0.00 4.75
2348 2453 4.458164 CGAAAAAGACGGCATGCC 57.542 55.556 27.67 27.67 0.00 4.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.